Bucs’ backup QB played for 49ers’ Jim Harbaugh

After rampant offseason speculation that the 49ers would trade for Harbaugh’s quarterback at the University of San Diego, the two will meet again Sunday when Tampa Bay visits Candlestick Park.

“Knowing the competitor that Josh is, we’ll say ‘hi’ before the game, give each other a big hug … then he’ll walk away and try to gouge our eyes out,” Harbaugh said Tuesday during his weekly appearance on KNBR. “He’s like a beloved son. And I hope he doesn’t beat us. We’ll be trying gouge his eyes out, too.”

Johnson, who will be an unrestricted free agent at the end of this season, played for Harbaugh at USD from 2004 through ’06. Even though USD was in Division I-AA (now FCS), Harbaugh termed Johnson the best quarterback in college football during his junior season.

An Oakland native, Johnson told The Chronicle in July that he’d welcome the chance to play for Harbaugh again.

“I’d get to come home, be with my family, play for a coach (who) changed my life and play for a team that I grew up loving,” he said.

Johnson, 25, the backup to Josh Freeman in Tampa Bay, has completed 1 of 3 passes for 7 yards this season.

Roster moves: The 49ers placed defensive tackle Will Tukuafu on injured reserve because of an undisclosed injury he sustained during Sunday’s win over the Eagles. To fill Tukuafu’s spot on the roster, rookie safety Colin Jones was promoted from the practice squad to the 53-man roster. The Niners also signed wide receiver John Matthews to the practice squad.

Tukuafu had appeared in all four games this season, collecting two tackles and grabbing a fumble recovery on his first NFL play in the season opener against Seattle. Jones, a sixth-round pick, is strictly a special-teams player. After playing in the season opener, he was released the following day and subsequently signed to the practice squad.

Matthews, who appeared in three games with Jacksonville last year, has spent time on the Colts’ practice squad. He played for Harbaugh from at USD (2005-06), making 46 catches for 1,049 yards and 13 touchdowns. He becomes the fourth member of the eight-man practice squad who played for Harbaugh in college.